[gmx-users] charge group moved too far between two domain decomposition steps?
Mark Abraham
mark.j.abraham at gmail.com
Wed Oct 22 05:20:15 CEST 2014
Hi,
You should start by using a time step more appropriate to your use of
constraints = none, or vice versa.
Mark
On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong <Kester2014 at ibs.re.kr> wrote:
> Dear all,
>
>
> I am intrigued by the error that I have received this morning, as follows:
>
>
>
> The charge group starting at atom 37920 moved more than the distance
> allowed by the domain decomposition (1.400000) in direction Y
>
> distance out of cell 7.144197
>
> Old coordinates: 54.499 39.697 14.058
>
> New coordinates: 54.499 39.697 14.058
>
> Old cell boundaries in direction Y: 19.468 32.846
>
> New cell boundaries in direction Y: 18.667 32.553
>
>
> If the charge group moved, if any, then shouldn't the new coordinates be
> showing different values?
>
> It was a new NPT calculation that I continued from a 20ns NVT run, so it
> should be equilibrated well enough, for a simple water on graphene system.
>
>
> Using GROMACS 5.0, I was unable to start the NPT with Berendsen
> thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my
> tau-T was 0.5, following the general rule of thumb, that tau-P should be
> larger than tau-T to allow thermal degrees of freedom to equilibrate faster
> than the box size).
>
>
> Should I reduce tau-P?
>
>
>
>
> Below is my NPT.mdp parameters:
>
> ; RUN CONTROL PARAMETERS
>
> integrator = md
>
> tinit = 20000.000
>
> dt = 0.002 ; 2 fs
>
> nsteps = 5000000 ; 10,000 ps
>
> comm-mode = Linear
>
> nstcomm = 10
>
>
> emtol = 0.001
>
> niter = 30
>
>
> ; OUTPUT CONTROL OPTIONS
>
> nstxout = 5000 ; save coordinates every 8 ps
>
> nstvout = 5000 ; save velocities every 8 ps
>
> nstfout = 0
>
> nstlog = 5000 ; update log file every 8 ps
>
> nstenergy = 5000 ; save energies every 8 ps
>
> ;nstxtcout is replaced with nstxout-compressed
>
> nstxout-compressed = 5000 ; no. of steps between writing
> coordinates using lossy compression
>
> ;xtc-precision is replaced with compressed-x-precision
>
> compressed-x-precision = 3000 ; precision with which to write to the
> compressed trajectory file
>
>
> ; Periodic boundary conditions: xyz (default), no (vacuum)
>
> cutoff-scheme = Verlet ; default for GROMACS-5.0
>
> nstlist = 1 ; A smaller nstlist may reduce LINCS
> warnings
>
> ns-type = grid ;
>
> pbc = xyz
>
> ;periodic_molecules = yes ; cannot be used with SHAKE
>
> ; nblist cut-off
>
> rlist = 1.40 ; short-range neighbourlist cutoff
>
> nstcalclr = 1
>
>
> coulombtype = PME
>
> coulomb-modifier = Potential-shift-Verlet
>
> r_coulomb = 1.40 ; short-range electrostatic cutoff
>
> rcoulomb-switch = 0 ; used when potential-switch
> (coulomb-modifier) is specified
>
> epsilon-r = 1 ; default value=1
>
> pme_order = 4
>
> fourierspacing = 0.12
>
> fourier_nx = 0
>
> fourier_ny = 0
>
> fourier_nz = 0
>
> ewald_rtol = 1e-05
>
> ewald_geometry = 3d
>
> epsilon_surface = 0 ; Use 0 when simulation is done with PME
>
>
>
> ;vdw-type = switch is replaced with the following two flags in GROMACS-5.0
>
> vdwtype = Cut-off
>
> vdw_modifier = Potential-switch
>
> ; cut-off lengths
>
> rvdw-switch = 1.00
> rvdw = 1.40 ; short-range van der Waals cutoff
>
> constraints = none
> constraint-algorithm = SHAKE
> continuation = yes ; starting from NVT run
> Shake-SOR = no
> shake-tol = 0.0001
> ;lincs-order = 4 ; accuracy of LINCS
> ;lincs-iter = 24 ; also related to accuracy
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> ;lincs-warnangle = 30
>
> Tcoupl = v-rescale
> nh-chain-length = 1 ; the leapfrog md integrator only supports
> 1
> ; Groups to couple separately
> tc-grps = GRA SOL
> ; Time constant (ps) and reference temperature (K)
> tau-t = 0.5 0.5
> ref-t = 300 300
> nsttcouple = 20 ; added by k-wong ; not specified in
> Yanbin's MDP
>
> Pcoupl = Parrinello-Rahman
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p = 5.0 ; time constant in ps
> compressibility = 4.5e-5 ; isothermal compressibility of water,
> bar^-1
> ref-p = 1.0 ; reference pressure, in bar
>
>
> ; Non-equilibrium MD stuff
> freezegrps = GRA
> freezedim = Y Y Y
>
> gen_vel = no
> ;gen_temp = 300
> ;gen_seed = 173529
>
>
> Thanks in advance!
>
>
>
> Regards,
>
> Kester
>
>
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